X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=c2be67ec89f89c7b83eed2d1444c7dfea7d1b0a2;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=896b60cc71a664ae456c888181546ba40147de43;hpb=69fff62bcf225887bbee81057099317a647be9be;p=jalview.git

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index 896b60c..c2be67e 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -1,11 +1,32 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.paradise;
 
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
-import jalview.ext.paradise.Annotate3D;
+import jalview.io.DataSourceType;
 import jalview.io.FastaFile;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.BufferedReader;
@@ -13,8 +34,9 @@ import java.io.File;
 import java.io.Reader;
 import java.util.Iterator;
 
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
 
 import MCview.PDBfile;
 
@@ -23,16 +45,17 @@ import compbio.util.FileUtil;
 public class TestAnnotate3D
 {
 
-  @Test
+  @Test(groups = { "Network" }, enabled = true)
   public void test1GIDbyId() throws Exception
   {
-    // use same ID as standard tests given at https://bitbucket.org/fjossinet/pyrna-rest-clients
+    // use same ID as standard tests given at
+    // https://bitbucket.org/fjossinet/pyrna-rest-clients
     Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
     assertTrue("Didn't retrieve 1GID by id.", ids != null);
-    testRNAMLcontent(ids,null);
+    testRNAMLcontent(ids, null);
   }
 
-  @Test
+  @Test(groups = { "Network" }, enabled = true)
   public void testIdVsContent2GIS() throws Exception
   {
     Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
@@ -51,9 +74,13 @@ public class TestAnnotate3D
         iline = id.readLine();
         fline = file.readLine();
         if (iline != null)
+        {
           System.out.println(iline);
+        }
         if (fline != null)
+        {
           System.out.println(fline);
+        }
         // next assert fails for latest RNAview - because the XMLID entries
         // change between file and ID based RNAML generation.
         assertTrue(
@@ -72,10 +99,11 @@ public class TestAnnotate3D
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Network" }, enabled = true)
   public void testPDBfileVsRNAML() throws Exception
   {
-    PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+    PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
+            DataSourceType.FILE);
     Assert.assertTrue(pdbf.isValid());
     // Comment - should add new FileParse constructor like new FileParse(Reader
     // ..). for direct reading
@@ -100,10 +128,12 @@ public class TestAnnotate3D
         sb.append(line + "\n");
       }
       assertTrue("No data returned by Annotate3D", sb.length() > 0);
-      AlignmentI al = new FormatAdapter().readFile(sb.toString(),
-              FormatAdapter.PASTE, "RNAML");
-      if (al==null || al.getHeight()==0) {
-        System.out.println(sb.toString());
+      final String lines = sb.toString();
+      AlignmentI al = new FormatAdapter().readFile(lines,
+              DataSourceType.PASTE, FileFormat.Rnaml);
+      if (al == null || al.getHeight() == 0)
+      {
+        System.out.println(lines);
       }
       assertTrue("No alignment returned.", al != null);
       assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
@@ -116,8 +146,9 @@ public class TestAnnotate3D
             String sq_ = new String(sq.getSequence()).toLowerCase();
             for (SequenceI _struseq : pdbf.getSeqsAsArray())
             {
-              if (new String(_struseq.getSequence()).toLowerCase().equals(
-                      sq_))
+              final String lowerCase = new String(_struseq.getSequence())
+                      .toLowerCase();
+              if (lowerCase.equals(sq_))
               {
                 struseq = _struseq;
                 break;
@@ -125,11 +156,13 @@ public class TestAnnotate3D
             }
             if (struseq == null)
             {
-              Assert.fail("Couldn't find this sequence in original input:\n"
-                      + new FastaFile().print(new SequenceI[]
-                      { sq })
-                      + "\n\nOriginal input:\n"
-                      + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");
+              AssertJUnit
+                      .fail("Couldn't find this sequence in original input:\n"
+                              + new FastaFile()
+                                      .print(new SequenceI[] { sq })
+                              + "\n\nOriginal input:\n"
+                              + new FastaFile().print(pdbf.getSeqsAsArray())
+                              + "\n");
             }
           }
         }